Analytical Report
SS200000135TL_D1
  • Summary
  • Square Bin
  • Cell Bin
  • Image
Spatial Gene Expression Distribution
Spatial gene expression distribution plot shows MID count at each spot (bin200)
Tissue Plot with Spot (bin200) Colored by MID Count
1,002,214,171
Total Reads
38,333
Mean MID per Bin200
6,403
Mean Gene per Bin200
108,123,310
Unique Reads
Key Metrices
Total Reads
Total number of sequenced reads
Valid CID Reads
Number of reads with CIDs matching the mask file and with MIDs passing QC
Invalid CID Reads
Number of reads with CIDs that cannot be matched with the mask file
Discarded MID Reads
Number of reads with MID that have been discarded since MID sequence quality does not satisfy with further analysis
Clean Reads
Number of Valid CID Reads that have passed QC
Non-Relevant Short Reads
Number of non-relevant short reads
Uniquely Mapped Reads
Number of reads that mapped uniquely to the reference genome
Multi-Mapped Reads
Number of reads that mapped more than one time on the genome
Unmapped Reads
Number of reads that cannot be mapped to the reference genome
Annotated Reads
Number of reads that are aligned to transcripts of at least one gene
Unannotated Reads
Number of reads that cannot be aligned to transcript of one gene
Total Reads
1,002,214,171
Valid CID Reads
818,079,170
Invalid CID Reads
175,869,912
Discarded MID Reads
8,265,089
Clean Reads
766,807,770
Non-Relevant Short Reads
51,271,400
Uniquely Mapped Reads
643,871,246
Multi-Mapped Reads
92,950,395
Unmapped Reads
29,986,129
Annotated Reads
532,386,027
Unannotated Reads
111,485,219
Information
Species
mouse
Tissue
brain
Reference
GRCm38.p6
FASTQ
E100026571_L01
Sequencing
Total Reads
Total number of sequenced reads
Total Q30
Ratio of bases with quality value exceeded 30 in the sequenced reads
CID Q30
Ratio of CID (Coordinate ID) bases with quality value exceeded 30
MID Q30
Ratio of MID (Molecule ID) bases with quality value exceeded 30
Total Reads
1,002,214,171
Total Q30
91.08%
CID Q30
91.74%
MID Q30
89.45%
Annotation
Exonic
Number of reads that mapped uniquely to an exonic region and on the same strand of the genome
Intronic
Number of reads that mapped uniquely to an intronic region and on the same strand of the genome
Intergenic
Number of reads that mapped uniquely to an intergenic region and on the same strand of the genome
Transcriptome
Number of reads that mapped to a unique gene in the transcriptome. These reads are considered for MID counting. (Transcriptome = Exonic + Intronic)
Antisense
Number of reads mapped to the transcriptome but on the opposite strand of their annotated gene
Exonic
483,163,052
Intronic
49,222,975
Intergenic
111,485,219
Transcriptome
532,386,027
Antisense
109,940,618
RNA Mapping
Clean Reads
Number of Valid CID Reads that have passed QC
Uniquely Mapped Reads
Number of reads that mapped uniquely to the reference genome
Multi-Mapped Reads
Number of reads that mapped more than one time on the genome
Unmapped Reads
Number of reads that cannot be mapped to the reference genome
Clean Reads
766,807,770
Uniquely Mapped Reads
643,871,246
Multi-Mapped Reads
92,950,395
Unmapped Reads
29,986,129
Tissue
DNB Under Tissue
Number of DNBs under tissue coverage region
mRNA-Captured DNBs Under Tissue
Number of DNBs under tissue that have captured mRNA
Genes Under Tissue
Number of detected gene under tissue coverage
Number of MID Under Tissue Coverage
Number of MID under tissue coverage
Fraction MID in Spots Under Tissue
Fraction of MID under tissue over total unique reads (MID Under Tissue / Unique Reads)
Reads Under Tissue
Number of reads with position prior to filtration under tissue coverage
Fraction Reads in Spots Under Tissue
Fraction of mapped reads under tissue over total mapped reads (Mapped Reads in Spots Under Tissue / (Valid CID Reads + Discarded MID Reads))
DNB Under Tissue
88,637,560
mRNA-Captured DNBs Under Tissue
36,679,634
Genes Under Tissue
24,299
Number of MID Under Tissue Coverage
89,816,137
Fraction MID in Spots Under Tissue
83.07%
Reads Under Tissue
648,371,996
Fraction Reads in Spots Under Tissue
78.46%
Sequencing Saturation
(left) Plot of the sequencing saturation as a function of sequencing depth(bin200)
(middle) Plot of the median number of genes detected per bin as a function of sequencing depth(bin200)
(right) Plot of the unique reads detected per bin as a function of sequencing depth(bin200)
Tissue Square Bin Statistics
Bin Size
The size of Bin which is the unit of aggregated DNBs in a squared region (i.e. Bin 50 = 50 * 50 DNBs)
Mean Reads (per bin)
Mean number of sequenced reads divided by the number of bins under tissue coverage
Median Reads (per bin)
Median number of sequenced reads divided by the number of bins under tissue coverage (pick the middle value after sorting)
Mean Gene Type (per bin)
Mean number of unique gene types divided by the number of bins under tissue coverage
Median Gene Type (per bin)
Median number of unique gene types divided by the number of bins under tissue coverage
Mean MID (per bin)
Mean number of MIDs divided by the number of bins under tissue coverage
Median MID (per bin)
Median number of MIDs divided by the number of bins under tissue coverage
Bin Size
Mean Reads
(per bin)
Median Reads
(per bin)
Mean Gene Type
(per bin)
Median Gene Type
(per bin)
Mean MID
(per bin)
Median MID
(per bin)
50
18,045
16,198
1,151
1,117
2,499
2,309
100
71,116
64,454
3,083
3,081
9,851
9,066
150
157,601
143,773
4,891
5,029
21,831
20,242
200
276,727
254,272
6,403
6,719
38,333
35,679
Bin 50
(left) Scatter plot of MID count and gene number in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene number in each bin
(bottom) Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis
Bin 100
(left) Scatter plot of MID count and gene number in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene number in each bin
(bottom) Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis
Bin 150
(left) Scatter plot of MID count and gene number in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene number in each bin
(bottom) Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis
Bin 200
(left) Scatter plot of MID count and gene number in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene number in each bin
(bottom) Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis
Clustering
(left) Clustering spots (bin200) under tissue covered with the Leiden algorithm
(right) UMAP projections of spots (bin200) colored by automated clustering. Same color is assigned to spots that are within shorter distance and with similar gene expression profile
Tissue Plot with Spots (bin200)
UMAP Projection of Spots (bin200)
Cell Bin Statistics
Mean/Median Cell Area
Mean/Median cell area (pixel)
Mean/Median Cell Boundary DNB Count
Mean/Median number of DNBs that have captured-mRNAs per cell
Mean/Median Gene Type
Mean/Median genes per cell
Mean/Median MID
Mean/Median MID count per cell
Mean Cell Area
286
Median Cell Area
270
Mean Cell Boundary DNB Count
282
Median Cell Boundary DNB Count
238
Mean Gene Type
229
Median Gene Type
201
Mean MID
411
Median MID
343
Cell Bin
(left) Scatter plot of MID count and gene number in each bin
(right) Violin plots show the distribution of deduplicated MID count and gene number in each bin
(bottom) Univariate distribution of MID count, gene numbers, and DNB numbers with rug along the x axis
Clustering
(left) Clustering spots (cell bin) under tissue covered region with the Leiden algorithm
(right) UMAP projections of spots (cell bin) colored by automated clustering. Spots in the short distance are assigned with the same color have similar gene expression profile.
Tissue Plot with Spots (cell bin)
UMAP Projection of Spots (cellbin)
Image Information
Manufacture
motic
Model
MoticamS6 M
Scan Time
2021-11-25 12:26:19
Overlap
0.1
Exposure Time (ms)
19.009
Scan Rows
13
Scan Columns
9
FOV Height
2,039
FOV Width
3,064
Stain Type
ssDNA
Stitched Image
No
Image Name
SS200000135TL_D1_20220527_201353_1.1.0
Stitching
Template Source Row No.
The row number of the template FOV used for predicting the entire template
Template Source Column No.
The column number of the template FOV used for predicting the entire template
Global Height
Height of the stitched image
Global Width
Width of the stitched image
Template Source Row No.
9
Template Source Column No.
6
Global Height
24,071
Global Width
25,128
QC
ImageQC version
ImageQC version
QC Pass
Whether the image(s) passed imageQC quality check
Track Line Score
Reference score for track line detection
Clarity Score
Reference score for image clarity
Good FOV Count
Number of FOVs that have at least one track dot detected
Total FOV Count
Total number of FOVs
Stitching Score
Reference score for stitching
Tissue Segmentation Score
Reference score for tissue segmentation
Registration Score
Reference score for aligning image with gene expression matrix
ImageQC Version
1.1.0
QC Pass
Pass
Track Line Score
70
Clarity Score
94
Good FOV Count
92
Total FOV Count
117
Stitching Score
93
Tissue Segmentation Score
95
Registration Score
99
Registration
ScaleX
The lateral scaling between image and template
ScaleY
The longitudinal scaling between image and template
Rotation
The rotation angle of the image relative to the template
Flip
Whether the image is flipped horizontally
Image X Offset
Offset between image and matrix in x direction
Image Y Offset
Offset between image and matrix in y direction
Counter Clockwise Rotation
Counter clockwise rotation angle
Matrix X Start
Gene expression matrix offset in x direction by DNB numbers
Matrix Y Start
Gene expression matrix offset in y direction by DNB numbers
Matrix Height
Gene expression matrix height
Matrix Width
Gene expression matrix width
ScaleX
0.866
ScaleY
0.866
Rotation
-1.603
Flip
True
Image X Offset
-3,383.29
Image Y Offset
2,065
Counter Clockwise Rotation
90
Matrix X Offset
0.00
Matrix Y Offset
0.00
Matrix Height
26,459
Matrix Width
26,459
Horizontal Image Stitching Deviation Heatmap
Image stitching deviation in the horizontal axis, a lighter color indicates better stitching
Vertical Image Stitching Deviation Heatmap
Image stitching deviation in the vertical axis, a lighter color indicates better stitching
SAW_v5.1.3
V2.0.2
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